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PDBsum entry 2qcc
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References listed in PDB file
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Key reference
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Title
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Structures of the human orotidine-5'-Monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
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Authors
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J.G.Wittmann,
D.Heinrich,
K.Gasow,
A.Frey,
U.Diederichsen,
M.G.Rudolph.
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Ref.
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Structure, 2008,
16,
82-92.
[DOI no: ]
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PubMed id
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Abstract
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UMP synthase (UMPS) catalyzes the last two steps of de novo pyrimidine
nucleotide synthesis and is a potential cancer drug target. The C-terminal
domain of UMPS is orotidine-5'-monophosphate decarboxylase (OMPD), a
cofactor-less yet extremely efficient enzyme. Studies of OMPDs from
micro-organisms led to the proposal of several noncovalent decarboxylation
mechanisms via high-energy intermediates. We describe nine crystal structures of
human OMPD in complex with substrate, product, and nucleotide inhibitors.
Unexpectedly, simple compounds can replace the natural nucleotides and induce a
closed conformation of OMPD, defining a tripartite catalytic site. The
structures outline the requirements drugs must meet to maximize therapeutic
effects and minimize cross-species activity. Chemical mimicry by iodide
identified a CO(2) product binding site. Plasticity of catalytic residues and a
covalent OMPD-UMP complex prompt a reevaluation of the prevailing
decarboxylation mechanism in favor of covalent intermediates. This mechanism can
also explain the observed catalytic promiscuity of OMPD.
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Figure 1.
Figure 1. UMPS Domain Structure and OMPD Biochemistry
(A) Reaction catalyzed by OMPD.
(B) Turnover of OMP
substrate by wild-type OMPD (black) is abolished in the
Asp312Asn mutant (red). If the detection limit of the assay is
assumed to be 5% of the total signal over 4000 s, the Asp312Asn
mutant is at least 1300-fold less active than the wild-type.
(C) Michaelis-Menten kinetics of wild-type OMPD at
25°C.
(D) OMPD is an obligatory dimer of high affinity.
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Figure 4.
Figure 4. Substrate Binding to OMPD
(A and B) Stereo
representation of the Asp312Asn OMPD-OMP complex showing a bent
carboxylate group.
(C and D) Stereo representation of the
Asp312Asn 6-HMUMP-OMPD complex. The hydroxymethyl group is also
bent out of plane, indicating that electrostatic repulsion by
Asp317b is not responsible for substrate deformation.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2008,
16,
82-92)
copyright 2008.
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